python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_Testis_atac-GSM5668080.end1.fastq.gz Bat3_Testis_atac-GSM5668080.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_Testis_atac-GSM5668080.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_wM1_atac-GSM5668081.end1.fastq.gz Bat3_wM1_atac-GSM5668081.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_wM1_atac-GSM5668081.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_Cerebellum_atac-GSM5668073.end1.fastq.gz Bat3_Cerebellum_atac-GSM5668073.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_Cerebellum_atac-GSM5668073.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_Liver_atac-GSM5668074.end1.fastq.gz Bat3_Liver_atac-GSM5668074.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_Liver_atac-GSM5668074.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_Muscle_atac-GSM5668075.end1.fastq.gz Bat3_Muscle_atac-GSM5668075.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_Muscle_atac-GSM5668075.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_ofM1_atac-GSM5668076.end1.fastq.gz Bat3_ofM1_atac-GSM5668076.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_ofM1_atac-GSM5668076.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_PreM_atac-GSM5668077-all.end1.fastq.gz Bat3_PreM_atac-GSM5668077-all.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_PreM_atac-GSM5668077-all.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_Putamen_atac-GSM5668079.end1.fastq.gz Bat3_Putamen_atac-GSM5668079.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_Putamen_atac-GSM5668079.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_2A_atac-GSM5668062.end1.fastq.gz Bat1_2A_atac-GSM5668062.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_2A_atac-GSM5668062.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_Caudate_atac-GSM5668068.end1.fastq.gz Bat1_Caudate_atac-GSM5668068.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_Caudate_atac-GSM5668068.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_Cerebellum_atac-GSM5668063.end1.fastq.gz Bat1_Cerebellum_atac-GSM5668063.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_Cerebellum_atac-GSM5668063.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_Liver_atac-GSM5668064.end1.fastq.gz Bat1_Liver_atac-GSM5668064.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_Liver_atac-GSM5668064.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_Muscle_atac-GSM5668065.end1.fastq.gz Bat1_Muscle_atac-GSM5668065.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_Muscle_atac-GSM5668065.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_ofM1_atac-GSM5668066.end1.fastq.gz Bat1_ofM1_atac-GSM5668066.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_ofM1_atac-GSM5668066.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_PreM_atac-GSM5668067.end1.fastq.gz Bat1_PreM_atac-GSM5668067.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_PreM_atac-GSM5668067.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_Putamen_atac-GSM5668069.end1.fastq.gz Bat1_Putamen_atac-GSM5668069.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_Putamen_atac-GSM5668069.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_Testis_atac-GSM5668070.end1.fastq.gz Bat1_Testis_atac-GSM5668070.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_Testis_atac-GSM5668070.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat1_wM1_atac-GSM5668071.end1.fastq.gz Bat1_wM1_atac-GSM5668071.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat1_wM1_atac-GSM5668071.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_2A_atac-GSM5668072.end1.fastq.gz Bat3_2A_atac-GSM5668072.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_2A_atac-GSM5668072.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Bat3_Caudate_atac-GSM5668078.end1.fastq.gz Bat3_Caudate_atac-GSM5668078.end2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -F4 -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Mammals/Rousettus_aegyptiacus-mRouAeg1.p/bowtie-indexes/GCF_014176215.1_mRouAeg1.p_genomic.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - Bat3_Caudate_atac-GSM5668078.2x36mers.GCF_014176215.1_mRouAeg1.p_genomic.unique